Microbiology Mysteries

Preface: An Introduction to Microbiology Mysteries

CHAPTER

1. Introduction to Microbiology, History of Microbiology
Disproving Spontaneous Generation
What Is Microbiology?
What Makes Up Microbiology?
What Is the Definition of Life?
Three Domains of Life
Naming of Living Things
Bacteria
Archaea
Eukaryotic Organisms
Fungi
Protists
Animals
Acellular Microbes
History of Microbiology
Outbreaks
Antonie van Leeuwenhoek
Edward Jenner
Louis Pasteur
Robert Koch and Koch’s Postulates
Martinus Beijerinck
Hans Gram
The Hesses—Fanny and Walther
Ignaz Semmelweis
Dmitri Ivanovsky
Joseph Lister
Paul Ehrlich and the First Antibacterial Medication
Emil von Behring
Alexander Fleming
Ernst Boris Chain and Howard Florey
Rebecca Lancefield
Stanley Prusiner

2. Applications of Microbiology
GI Outbreak in a New Neighborhood
What Can Microbiology Actually Accomplish?
Medical
Industrial
Fermentation and Fermenters
Describe Steps
How to Optimize
Product Collection
Product Processing and Purification
Large-Scale Productions of Chemicals
Biotechnology
DNA Analysis
Protein Analysis
Genetically Modified Organisms
Food
Environmental

3. Strategies for Identification and Diagnosis
Creating an Identification Key for Gram-Negative Rods
Steps of Identification or Diagnosis
Sample Collection and Processing
Inoculation of Samples
Incubation and Growth of Samples
Isolation of Microbes
Viewing Microbes
Microscopic
Types of Microscopy
Slide Preparations to View Live Bacteria
Information Collection
Biochemical
Genetic
Serological
Phage Typing
Identification

4. Cultivating and Measuring Microbial Growth in the Laboratory
Trouble Growing Bacteria
Bacterial Growth
Bacterial Binary Fission
Bacterial Growth Curve
Measuring Microbial Growth
Turbidometry
Plate Counts
Flow Cytometry
Most Probable Number
Eukaryotic Growth and Reproduction
Mitosis and Meiosis
Conditions for Growth
The Importance of Aseptic Techniques and Minimizing Contamination
Temperature
pH
Nutrients—Note Roles and Why They Are Needed
Macronutrients
Micronutrients
Moisture
Barometric Pressure
Osmotic Pressure
Growth Media for Bacteria
Types of Media Based on Structure
Types of Media Based on Preparation
Types of Media Based on Chemical Composition
Types of Media Based on Function—Note to Appendix of Common Media
Growth Media for Eukaryotic Cell Cultures
Growth Conditions—How They Differ from Bacteria, List If Relevant
Growth of Viruses

5. Survey of Prokaryotic Organisms
Sick Trip to Vegas
What Are Prokaryotic Organisms?
Basic Definition
Size of Bacterial Cells Compared to Other Organisms
How Many?
Known Species
Pathogenic Species
Theorized Numbers of Species
Prokaryotic Cell Structure
Fimbriae
Pili
Glycocalyx
Capsule
Wax Layer
Slime Layer
Cell Wall—Chemical Differences and Disease Impact
Gram-positive
Gram-negative
Acid-fast
Pleomorphic—No Cell Wall
Cell Membrane
Cytoplasm
Inclusions or Granules
Ribosomes
Nucleoid
DNA
Plasmids
Flagella
Axial filaments

6. Survey of Eukaryotic Organisms
Be Careful Who Catches Your Fish
History and Significance of Eukaryotic Organisms
Eukaryotic Cell Structure
Cell Membrane with Proteins
Cell Wall
Cytoskeleton
Centrioles
Cytoplasm
Ribosomes
Glycocalyx
Extracellular matrix (ECM)
Nucleus
Nucleolus
Smooth Endoplasmic Reticulum (ER)
Rough ER
Golgi
Mitochondria
Chloroplast
Vacuoles
Lysosomes
Flagella
Cilia
Classes of Eukaryotic Organisms of Note
Fungi
Structure
Classes of Fungi
Protists
Algae
Protozoans
Arthropods
Helminths
Roundworms (Nematodes)
Flatworms
Benefits and Consequences of Eukaryotic Organisms
Benefits
Consequences

7. Survey of Acellular Microbes
Re-Emergent Ebola
What Are Acellular Microbes?
Viruses
Types of Viruses—Define What They Infect and Provide Examples
Structure
Capsid
Nucleic Acid
Proteins
Envelope
Basis of Virus Classification
Infection Patterns
Bacteriophage
Animal
Effects of Virus Infection
Transformation and Cancer
Disease Patterns
Satellite Viruses
Viroids
Prions

8. Microbial Metabolism
Drunk without Drinking
What Is Metabolism?
Origins of Metabolism in Microbes
Chemistry of Metabolism
Enzymes
Why They Are Needed and Need to Work
Structure and Function and Importance of Active Site
Cofactors
Reaction Rates
Factors That Impact Reaction Rates/Enzyme Function
Regulation
Types of Enzymes (make a chart) Based on Functions
Oxidation and Reduction
Electron Transport
Anabolic and Catabolic Reactions
ATP Generation and ATP Cycle
Types of Catabolic Metabolism
Locations of Respiration and Fermentation Reactions
How Can We Test Metabolic Reactions in the Laboratory?
Glycolysis
Fates of Pyruvate
Fermentation
Oxidation/Respiration
Variations of Catabolism
Anabolic Metabolism
Gluconeogenesis
Glycogenolysis
Photosynthesis
Light-Dependent Reactions
Dark Reactions

9. Microbial Genetics and Biotechnology
Brain-Eating Ameba in a Strange Place
What Is Genetics?
Microbial Genome Sizes
Bacterial Molecular Biology
Flow of information—DNA → RNA → Protein
DNA Structure
DNA Replication
Transcription
Translation and the Genetic Code
Mutations
Testing for Mutagens
Genetic Regulation
RNA Splicing—Eukaryotic Organisms
Transposons
Biotechnology
What Is Biotechnology?
Applications of Biotechnology
Industrial
Medical
Food
Plants and Animals—GMOs
Recombinant DNA
What Is It?
How Is It Made?
Other Methods
DNA Analysis
Proteins
Hybridization
PCR
Sequencing
DNA Fingerprinting

10. Mechanisms of Prokaryotic Disease and the Disease Process
Contaminated Fish
What Is a Disease?
Define a Disease
Types of Diseases
Earliest Known Diseases Reported
Historically Significant Outbreaks
Bacterial Symbiosis
Symbiotic
Parasitism
Commensalism
Mutualism
Nonsymbiotic
Synergism
Antagonism
How Do Microbes Cause Disease?
Why Doesn’t Disease Always Occur?
ID50
LD50
Strength of Immune System
Vaccinations
Preferred Portal of Entry for Microbes
Virulence Factors
Prokaryotic
Enzymes
Toxins
Cellular Factors
Disease Process
What Is a Disease?
Signs versus Symptoms
The Disease Process and Stages
Incubatory
Prodromal
Period of Disease
Convalescent Period
Types of Infections
Localized
Systemic
Focal
Types of Disease
Acute
Chronic
Subacute
Latent
Level of Infections

11. Transmission of Diseases and Epidemiology
Measles Outbreak—MMWR Activity
Hospital-Associated Infections (HAIs)
What Are Health-Care-Associated Infections (HAIs)?
What Bacteria Cause Them?
Why Do They Occur?
Where Do They Occur?
Death Rates of Infections
Who Is at Risk?
Disease Transmission
What Is Disease Transmission?
Chain of Infection
Why Doesn’t Disease Always Occur?
Communicable versus Contagious
Patient Containment and Precautions
Role of Health-Care Workers in Controlling Infections
Universal Precautions
Specialized Precautions
Epidemiology
Important Terms
Types of Outbreaks
Types of Disease Outbreak Patterns
How to Calculate Disease Risks

12. Physical and Chemical Methods of Control
Hand Washing without Soap
About Bacterial Control
Terminology
Stability/Resistance to Treatment of Microbes
Factors Impacting Control Methods
Targets of Action of Physical and Chemical Methods of Control
Differences between Physical and Chemical Methods of Control
Physical Methods of Control
Desiccation
Radiation
Filtration
Chemical Methods of Control
Types
Alcohols
Halogens
Phenols
Bisbiguanides
Quats
Soaps
Metals
Aldehydes
Gases
Acids and Bases

13. Antimicrobial Treatment Strategies, Superbugs
Typhoid Fever Outbreak
Introduction
Define
What makes an ideal drug?
Spectrum of action
Effects
Bacteriostatic
Bactericidal
What Can Be Treated with Antimicrobial Drugs?
Drug Development
History
Early research
Alexander Fleming and the discovery of penicillin
How are drugs screened and developed?
Knowledge of naturally occurring drugs
How long does it take and how much does it cost for a drug to be developed, approved, and sent to
market?
Preclinical trials
Clinical trials
Antibacterial Drugs
Mechanisms of action
Cell wall inhibitors
Cell membrane disruptors/inhibitors
Protein synthesis inhibitors
Nucleic acid synthesis inhibitors
Metabolic pathway inhibitors
Newer drugs
Potential side effects
Antiprotozoal Drugs
Antifungal Drugs
Antihelminth Drugs
Antiviral Drugs
History
Why they are difficult to develop
Mechanisms of action—list based on mechanisms and diseases
HIV
Influenza
Herpes family
Resistance
Genetic basis of resistance
Mechanisms of resistance in bacteria
Efflux pumps
Changing binding sites
Changing shape of target molecule
Enzymes that convert antibiotics to nonfunctional molecules
Going around blocked metabolic pathways
Superbugs
Examples
Mechanisms of resistance in other microbes
Impact of resistance
Lack of antibiotic development
Measuring antibiotic susceptibility
Kirby-Bauer (disk diffusion) test
Minimum inhibitory concentration (MIC)
Therapeutic index

14. Nonspecific Defenses
Tracking the Source of a Nursing Home Outbreak
What Is Immunity?
Level 1—Nonspecific
Level 2—Nonspecific
Introduction to white blood cells and the immune system
The nonspecific cells
Functions of the second line of defense
Phagocytosis
Inflammation
Acute versus chronic inflammation
Fever
Complement
Interferons

15. Specific Defenses
HIV Noninfection
Three levels of immune defenses
Specific defenses
Aspects
Antigens
Importance of antigen-presenting cells (APCs)
The two arms of specific immunity
Where do specific immune responses occur?
Cells involved in specific responses
T cells—cell-mediated
B cells—Humoral
Development of Immune cells
B cells
How does the immune response tie together?
Acquiring immunity and roles of specific cells
Value and significance of vaccinations
History of vaccines
Mechanism of action
Why boosters may be required
Types of vaccines
Herd immunity
List of vaccines given
Childhood vaccination schedule
Vaccines that are optional
Side effects
Controversy

16. Disorders of the Immune System
Peanut Allergy “Treatment”
About the Immune System and Why It Overreacts
Types of Disorders
Hypersensitivities
Autoimmune Diseases
Immunodeficiencies
Primary immunodeficiencies
Secondary immunodeficiencies
Cancers of the blood/immune system

Appendices
1. List of Important Microbial Diseases
2. Important Staining Techniques
3. Common Differential Tests and Growth Media
4. The Taxonomy of the Domain Bacteria
5. The Taxonomy of the Domain Archaea
6. The Taxonomy of the Domain Eukarya